Cottus confusus
Shorthead sculpin
GC content
46.27%
Whole genome
Non-coding
935 bp
D-loop 853 bp
Where Shorthead sculpin sits among 2,335 species
Whole-genome GC content against maximum lifespan. Shorthead sculpin has the 1,938th longest lifespan of them.
- This species
- Other ray-finned fishes
- Other classes
Base composition
Whole genome16,533 bp
- GC skew (G − C) / (G + C)
- −0.282
- AT skew (A − T) / (A + T)
- +0.021
About this record
- Lifespan source
- AnAge build 15
- Based on
- an animal in the wild
- Data quality
- acceptable, medium sample
- Licence
- Free to use, subject to the Human Ageing Genomic Resources conditions of use
- Status
- New in build 2
- In the database since
- build 2 (2026-11-13)
Every change against the 2015 build is in the changelog download.
Composition by region
Reference (L) strand as deposited in RefSeqWhole genome16,533 bp
Protein-coding11,407 bp
12S rRNA947 bp
16S rRNA1,691 bp
All tRNA1,553 bp
D-loop853 bp
Genes and regions
Select a column to sort; select a gene to compare it across species| Composition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| ND1NADH dehydrogenase subunit 1 | 975 bp | 48.62% | −0.363 | −0.102 | |||||
| ND2NADH dehydrogenase subunit 2 | 1,045 bp | 46.79% | −0.476 | +0.018 | |||||
| COX1Cytochrome c oxidase subunit I | 1,551 bp | 46.23% | −0.211 | −0.120 | |||||
| COX2Cytochrome c oxidase subunit II | 691 bp | 45.30% | −0.304 | +0.037 | |||||
| ATP8ATP synthase F0 subunit 8 | 168 bp | 48.81% | −0.537 | +0.209 | |||||
| ATP6ATP synthase F0 subunit 6 | 684 bp | 47.22% | −0.467 | −0.075 | |||||
| COX3Cytochrome c oxidase subunit III | 786 bp | 48.35% | −0.268 | −0.054 | |||||
| ND3NADH dehydrogenase subunit 3 | 349 bp | 49.28% | −0.267 | −0.288 | |||||
| ND4LNADH dehydrogenase subunit 4L | 297 bp | 48.15% | −0.399 | −0.117 | |||||
| ND4NADH dehydrogenase subunit 4 | 1,381 bp | 46.85% | −0.360 | −0.057 | |||||
| ND5NADH dehydrogenase subunit 5 | 1,839 bp | 44.43% | −0.405 | −0.008 | |||||
| ND6NADH dehydrogenase subunit 6 | 522 bp | 46.55% | −0.424 | +0.427 | |||||
| CYTBCytochrome b | 1,141 bp | 48.38% | −0.341 | −0.090 | |||||
| 12S rRNA12S ribosomal RNA | 947 bp | 47.84% | −0.108 | +0.219 | |||||
| 16S rRNA16S ribosomal RNA | 1,691 bp | 45.83% | −0.099 | +0.199 | |||||
| D-loopControl region (D-loop) | 853 bp | 36.93% | −0.098 | +0.007 |
Codon usage
Counts per codon, darker is more frequent3,808 codons in all protein-coding genes. Grouped with the Vertebrate mitochondrial code (NCBI table 2).
Phe F6.2%
UUU122
UUC113
Leu L17.4%
UUA75
UUG29
CUU178
CUC164
CUA172
CUG44
Ile I6.8%
AUU139
AUC120
Met M3.9%
AUA99
AUG50
Val V5.9%
GUU69
GUC46
GUA77
GUG31
Ser S6.5%
UCU59
UCC67
UCA54
UCG9
AGU10
AGC49
Pro P5.8%
CCU67
CCC103
CCA45
CCG5
Thr T8.6%
ACU51
ACC153
ACA110
ACG12
Ala A8.7%
GCU68
GCC176
GCA83
GCG5
Tyr Y2.9%
UAU40
UAC69
His H2.8%
CAU31
CAC76
Gln Q2.7%
CAA82
CAG19
Asn N3.2%
AAU29
AAC91
Lys K1.9%
AAA59
AAG13
Asp D1.9%
GAU17
GAC56
Glu E2.6%
GAA77
GAG23
Cys C0.6%
UGU9
UGC15
Trp W3.2%
UGA95
UGG25
Arg R2.0%
CGU12
CGC18
CGA37
CGG9
Gly G6.4%
GGU40
GGC81
GGA68
GGG55
Stop 0.2%
UAA6
UAG2
AGA0
AGG0
Genome map
38 annotated features in NC_066922.1Hover, tap or tab to a feature to see its position, length, strand and GC content. Genes and rRNAs open their own pages.
- Protein-coding13
- rRNA2
- tRNA22
- D-loop1
- Outer ring: + strand, arrows run clockwise. Inner ring: − strand.
- Middle ring: GC% of each gene against the whole genome (46.3%, dashed): out is GC-richer, in is AT-richer (full height = 6 points).
All 38 features as a table
| Feature | Type | Start | End | Length | Strand | GC |
|---|---|---|---|---|---|---|
| tRNA-Phe | Transfer RNA | 1 | 70 | 70 bp | + | – |
| 12S rRNA | Ribosomal RNA | 71 | 1,017 | 947 bp | + | 47.8% |
| tRNA-Val | Transfer RNA | 1,018 | 1,089 | 72 bp | + | – |
| 16S rRNA | Ribosomal RNA | 1,090 | 2,780 | 1,691 bp | + | 45.8% |
| tRNA-Leu (UUR) | Transfer RNA | 2,781 | 2,854 | 74 bp | + | – |
| ND1 | Protein-coding gene | 2,855 | 3,829 | 975 bp | + | 48.6% |
| tRNA-Ile | Transfer RNA | 3,834 | 3,903 | 70 bp | + | – |
| tRNA-Gln | Transfer RNA | 3,903 | 3,973 | 71 bp | − | – |
| tRNA-Met | Transfer RNA | 3,973 | 4,042 | 70 bp | + | – |
| ND2 | Protein-coding gene | 4,043 | 5,087 | 1,045 bp | + | 46.8% |
| tRNA-Trp | Transfer RNA | 5,088 | 5,158 | 71 bp | + | – |
| tRNA-Ala | Transfer RNA | 5,160 | 5,228 | 69 bp | − | – |
| tRNA-Asn | Transfer RNA | 5,230 | 5,302 | 73 bp | − | – |
| tRNA-Cys | Transfer RNA | 5,340 | 5,406 | 67 bp | − | – |
| tRNA-Tyr | Transfer RNA | 5,407 | 5,476 | 70 bp | − | – |
| COX1 | Protein-coding gene | 5,478 | 7,028 | 1,551 bp | + | 46.2% |
| tRNA-Ser (UCN) | Transfer RNA | 7,029 | 7,099 | 71 bp | − | – |
| tRNA-Asp | Transfer RNA | 7,103 | 7,175 | 73 bp | + | – |
| COX2 | Protein-coding gene | 7,199 | 7,889 | 691 bp | + | 45.3% |
| tRNA-Lys | Transfer RNA | 7,890 | 7,963 | 74 bp | + | – |
| ATP8 | Protein-coding gene | 7,965 | 8,132 | 168 bp | + | 48.8% |
| ATP6 | Protein-coding gene | 8,123 | 8,806 | 684 bp | + | 47.2% |
| COX3 | Protein-coding gene | 8,806 | 9,591 | 786 bp | + | 48.4% |
| tRNA-Gly | Transfer RNA | 9,592 | 9,663 | 72 bp | + | – |
| ND3 | Protein-coding gene | 9,664 | 10,012 | 349 bp | + | 49.3% |
| tRNA-Arg | Transfer RNA | 10,013 | 10,082 | 70 bp | + | – |
| ND4L | Protein-coding gene | 10,083 | 10,379 | 297 bp | + | 48.2% |
| ND4 | Protein-coding gene | 10,373 | 11,753 | 1,381 bp | + | 46.9% |
| tRNA-His | Transfer RNA | 11,754 | 11,822 | 69 bp | + | – |
| tRNA-Ser (AGY) | Transfer RNA | 11,823 | 11,890 | 68 bp | + | – |
| tRNA-Leu (CUN) | Transfer RNA | 11,895 | 11,967 | 73 bp | + | – |
| ND5 | Protein-coding gene | 11,968 | 13,806 | 1,839 bp | + | 44.4% |
| ND6 | Protein-coding gene | 13,803 | 14,324 | 522 bp | − | 46.6% |
| tRNA-Glu | Transfer RNA | 14,325 | 14,393 | 69 bp | − | – |
| CYTB | Protein-coding gene | 14,398 | 15,538 | 1,141 bp | + | 48.4% |
| tRNA-Thr | Transfer RNA | 15,539 | 15,610 | 72 bp | + | – |
| tRNA-Pro | Transfer RNA | 15,614 | 15,680 | 67 bp | − | – |
| D-loop | Control region | 15,681 | 16,533 | 853 bp | – | 36.9% |